They never been conditioned. How do I condition them? What do i use? And how long do I condition both of them for? And my female betta was in the jar inside of the 40 gallon tank for 2 day with the male in the tank.

Conditioning is feeding the breeding pair with highly nutritious food which is provided by live or frozen foods. If you feed them these types of food regularly, they are constantly conditioned and you can breed them any time. Otherwise you need to fatten them up for about 2 weeks or so because (specially the male) will need extra energy rearing eggs and fry.